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Chipotle Butternut Squash Enchiladas

5 from 1 vote

Published Nov 03, 2025

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These Chipotle Butternut Squash Enchiladas are hands down the best vegetarian enchilada out there. Smoky spiced flavors from the chipotle married with sweet earthy butternut squash make for a flavor combination you will love. They come together quickly, heat up well as leftovers and are all around a comfort meal without the guilt.

Why Make These Vegetarian Enchiladas
Ingredient Notes
Steps To Make Vegetarian Enchiladas
Chipotle Butternut Squash Enchilada Tips
Chipotle Butternut Squash Enchiladas Recipe
Other Cozy meals to try

Why Make These Vegetarian Enchiladas

I am always looking for a good vegetarian dish to throw into the weeknight mix, we eat a lot of meat in my household so it’s nice to take a little break every once in awhile.

Full of flavor & Texture. The flavor combo will leave you satisfied and not craving meat! and the textures are complex which I love with every recipe I make.
Meal Prep Friendly. They heat up great if you have leftovers, and they travel well.
Perfect for seasonal produce. You can really add any veggies into these, but it’s a great way to enjoy butternut squash o sweet potatoes as the seasons change.
Other great recipes with squash to try, Butternut Squash & Feta Salad, Squash Quinoa Salad, Squash Gnocchi. All of them are wonderful!

Ingredient Notes

Ingredients needed to make this recipe on a marble counter top.

All other ingredients and measurements can be found in the recipe card towards the bottom of this post.

Butternut Squash. Use fresh roasted squash or cut the time and effort down and grab some frozen squash at the grocery store. Sweet potatoes also work great for this recipe.
Chipotle Peppers. You can find these in the international aisle at the store, they can be spicy so opt for the mild if you are sensitive to heat. You can also just use chipotle seasoning if you’d prefer.
Black Beans. I use canned, they will be rinsed and drained.
Fresh Tomatoes. Chopped, they add color and a little liquid to the mix.
Onion.
Seasonings.
Red Enchilada Sauce. Please choose your favorite premade sauce for this recipe.
Corn Tortillas. This is the traditional tortilla for enchilada’s but flour will also work well if you’d like!

Steps To Make Vegetarian Enchiladas

Ready to cook? Let me walk you through the recipe. For your convenience, there is a full ingredient list and detailed instructions in the printable recipe card below.

Step One. Heat up the butternut squash, if using frozen, put it in the microwave for about half the time the page calls for to soften them up. If you have fresh roasted squash, skip the the next step.
Step Two. Preheat the oven to 375º. Grab a large skillet and heat the oil on medium/high heat.
Step Three. Add chopped onions to the skillet, sauté for about 2 minutes. Next add in the seasonings, beans, tomatoes, chipotle peppers, squash.
Step Four. Sauté on medium heat for about 4 minutes, feel free to mash everything together just a bit so it fits into the tortillas better. Take it off the heat and prepare the vegetarian enchiladas.
Step Five. Grab a large baking dish, put about 1/4 cup of red enchilada sauce on the bottom (this helps everything from sticking to the baking dish)
Step Six. Roll up the enchiladas! Try not to over stuff them, otherwise they can crack. Snuggle them up into the baking dish.

Step Seven. Once they are all ready and stuffed, pour the leftover enchilada sauce over them and sprinkle well with shredded cheese. Bake for about 20 minutes or until the cheese is melted, and the sauce is bubbling. Serve with your favorite toppings and enjoy!

Chipotle Butternut Squash Enchilada Tips

Add more veggies. If you want, add some chopped mushroom or bell pepper. Even chopped spinach makes a nice addition.
Do not over stuff the tortillas, they will crack and break if they have too much filling.
Preheat the tortillas. I add a damp paper towel around them and microwave for 45 seconds to help make them more forgiving and crack less.
Use chipotle powder if you are sensitive to heat. You can use 1 tsp of chipotle powder instead of the peppers in adobo sauce if you are very sensitive to heat.
Store leftovers in an airtight container in the fridge for up to 4 days. You can freeze these for up to 2 months.

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